title: DYRK2 knockout mice exhibit fetal growth retardation

status: Public on Apr 27 2020

city: Minato-ku

first: Satomi

last: Yogosawa

state: Tokyo

address: 3-25-8, Nishi-shinbasi

department: Department of Biochemistry

institute: Jikei University School of Medicine

summary: We generated DYRK2-deficient mice using the CRISPR/Cas9 genome editing method and demonstrated that loss of DYRK2 gene causes fetal growth retardation and neonatal lethality at birth. Total RNA from DYRK2-/- whole embryo was compared with those of WT mice by microarray.

overall_design: mRNA expression of whole embryo from DYRK2 knockout mice was compared with those of WT mice.

first: Kiyotsugu

last: Yoshida


title: Deconvoluting global cytokine signaling networks in natural killer cells [ChIP-Seq]

status: Public on May 01 2020

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

country: USA

institute: Cornell University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cytokine signaling via signal transducer and activator of transcription (STAT) proteins is crucial for optimal antiviral responses of natural killer (NK) cells. However, the pleiotropic effects of both cytokine and STAT signaling preclude the ability to precisely attribute molecular changes to either source. In this study, we employ a multi-“omics” approach to deconstruct and rebuild the complex interaction of three major STAT signaling pathways in NK cells. We uncover a global STAT4-STAT5 cooperative axis that is distinct and sometimes antagonistic to the STAT1 axis. We generate a network of STAT targets that highlights an integrated negative feedback loop, and demonstrate distinct STAT modes of epigenetic regulation. Finally, we identify shared signatures between mouse in vitro profiles and profiles from viral infection and humans, highlighting clinically translatable targets. Overall, we begin to unravel the intricate crosstalk between cytokine signaling pathways, and offer a valuable resource for improving cellular immunotherapy.

overall_design: ChIP-seq was performed on ex-vivo NK cells stimulated with various cytokine combinations.

middle: M

first: Joseph

middle: C

last: Sun


title: m6A methylation regulates the fate of endogenous retrovirus transcripts [RIP-seq]

status: Public on Apr 13 2020

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

country: France

institute: institut curie

type: Expression profiling by high throughput sequencing

summary: Using a genome-scale CRISPR knockout screening in mouse embryonic stem cells, we identify m6A RNA methylation as an important regulatory component that restricts the activity of endogenous retroviruses of the IAP (intracisternal A-particles) family. The m6A methylation of IAP mRNAs occurs on their 5’ end, is catalyzed by the complex of methyltransferase-like (METTL)3/METTL14 proteins whose depletion, along with other complex subunits, namely WTAP and ZC3H13, leads to increased IAP transcript abundance. Using auxin-dependent degron, we show that rapid removal of METTL3, METTL14 and ZC3H13 further increases IAP RNA abundance in a progressive and reversible fashion. Finally, we demonstrate that m6A RNA reduces the stability of IAP transcripts

overall_design: m6A-seq was measured from total RNA in mouse embryonic stem cells (ESCs) in WT and Mettl3-/- conditions. 3 biological replicates are available for the IP of m6A. One control input was generated per cell condition.

first: Tomasz

last: Chelmicki

first: Aurelie

last: Teissandier


title: Deconvoluting global cytokine signaling networks in natural killer cells

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Transcriptomic Characterization of Human Choroidal Neovascular Membranes Identifies Calprotectin as a Novel Biomarker for Patients with Age-related Macular Degeneration

status: Public on Apr 09 2020

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

country: Germany

institute: Uniklinik Freiburg

summary: Although genome-wide association studies, animal models, and cell culture systems have yielded important insights into the pathogenesis of neovascular age-related macular degeneration (nAMD), the underlying molecular pathways remain ill defined. Recent studies have deciphered the transcriptional profile of choroidal neovascularisation (CNV) of body donor eyes and were thus limited by the time span from death to preservation and the associated rapid 5'-RNA degradation. In this study, CNVs were therefore formalin-fixed immediately after surgical extraction from patients with nAMD and analyzed using a 3’ RNA sequencing approach called Massive Analysis of cDNA Ends (MACE). Age-matched formalin-fixed paraffin-embedded (FFPE) RPE-choroidal specimens obtained from the macular region of enucleated eyes with ciliary body melanoma served as controls. Transcriptome profiles were generated and disease-associated gene signatures were identified using statistical and bioinformatic methods. Calprotectin (S100A8/A9) protein expression was investigated by immunohistochemistry and ELISA.We identified 158 differentially-expressed genes (DEG) that were significantly increased in CNV compared to control tissue. Gene ontology enrichment analysis demonstrated that these DEG contributed to biological processes, such as Blood Vessel Development, Extracellular Structure Organization, Response to Wounding and several immune-related terms. The S100 calcium-binding protein A8 (S100A8) and S100A9 emerged among the top DEG, as confirmed by immunohistochemistry on CNV tissue and protein analysis of vitreous samples from nAMD patients and controls. This study provides a high-resolution RNA-sequencing-based transcriptional signature of choroidal neovascular membranes in AMD patients and reveals S100A8/A9 as a novel biomarker and promising target for AMD-directed therapeutics and diagnostics.

overall_design: MACE RNA sequencing of four human CNV-membranes (from patients undergoing subretinal CNV extraction) and four control samples

first: Anja

last: Schlecht

first: Stefaniya

last: Boneva

first: Markus

last: Gruber

first: Peipei

last: Zhang

first: Ralf

last: Horres

first: Felicitas

last: Bucher

first: Claudia

last: Auw-Haedrich

first: Lutz

last: Hansen

first: Andreas

last: Stahl

first: Ingo

last: Hilgendorf

first: Hansjürgen

last: Agostini

first: Peter

last: Wieghofer

first: Günther

last: Schlunck

first: Julian

last: Wolf


title: High-dimensional single cell analysis reveals an effector Treg molecular program that correlates with lung cancer progression

status: Public on Mar 03 2020

city: Rozzano

first: Simone

last: Puccio

state: Milan

address: Via Alessandro Manzoni, 56

country: Italy

institute: Humanitas Clinical and Research Center

summary: Anti-tumor immune responses are counteracted by CD4+ regulatory T (Treg) cells in the tumor micronenvironment, but the molecular mechanisms responsible for the enhanced suppressive activity of Tregs are poorly defined. High-dimensional single cell profiling of millions of single CD4+ and CD8+ T cells from 53 chemotherapy-na‹ve individuals with lung adenocarcinoma identified the transcription factor IRF4 as constitutively expressed by effector CD4+ Tregs present exclusively in tumors. These IRF4+, but not the quiescent IRF4_ÿTregs expressed a vast array of suppressive molecules, positively correlated with multiple inhibitory and exhausted subpopulations of T cells and were more abundant in rapidly progressing patients. Integration of transcriptomic data and whole genome binding sites of transcription factors further revealed that IRF4, either alone or in combination with its partner BATF, directly controlled a molecular program responsible for Treg hyperproliferation and suppressive functions that included CTLA-4, ICOS, TNFRSF9 (4-1BB) and IL1R2, previously shown to impact survival in lung cancer. Thus, interfering with the IRF4-dependent molecular program may represent a novel immunotherapeutic approach capable to block immunosuppression in the tumor microenvironment without inducing autoimmunity in peripheral tissues.ÿ

overall_design: Transcriptional profiling of human tumor infiltrating Tregs. Gene expression profile of facs sorted Tregs (CD4+CD25+CD127-CCR8+ICOS+ and CD4+CD25+CD127-CCR8-ICOS-) from 5 surgically resected and cryopreserved human non small-cell lung cancer carcinomas.

first: Giorgia

last: Alvisi

first: Jolanda

last: Brummelman

first: Elisa

last: Paoluzzi Tomada

first: Emilia

last: Mazza

first: Enrico

last: Lugli


title: Microglia transcriptome in a rat model of ischemic stroke

status: Public on Apr 24 2020

city: Boston

first: Wenjun

last: Deng

state: MA

address: 175 Cambridge street

institute: Massachusetts General Hospital

summary:
Microglia are key regulators of inflammatory response after stroke and brain injury. Here we profiled the microglia transcriptome isolated from a spontaneously hypertensive rat model of focal cerebral ischemia.
We identified an extensive and persistent upregulation of anti-inflammatory M2-like patterns after stroke and a mild up-regulation of pro-inflammatory M1-like patterns at later stage. We also found that younger brains showed larger microglial response than middle aged brains. Moreover, beyond the standard M1/M2 dichotomy, a wide spectrum of novel microglial polarization states was activated in response to stroke, particularly the phenotypes related to Tlr2 and dietary fatty acids stimulation.

overall_design: We analyzed microglial gene expression change from 3 to 14 days after stroke onset and compared the activation pattern between 3-month and 12-month old brains.

first: Emiri

last: Mandeville

first: Yasukazu

last: Terasaki

first: Wenlu

last: Li

first: Mingming

last: Ning

first: Eng

middle: H

last: Lo

first: Changhong

last: Xing


title: Sliced Human Cortical Organoids for Modeling Distinct Cortical Neuronal Layer Formation

status: Public on Mar 05 2020

city: Philadelphia

first: Yijing

last: Su

state: PA

address: Levy 326

department: Department of Oral Medicine

institute: University of Pennsylvania

summary: Brain organoids provide unique platforms for modeling development and diseases by recapitulating the architecture of the embryonic brain. However, current organoid methods are limited by interior hypoxia and cell death due to insufficient surface diffusion, preventing generation of architecture representative of late developmental stages. Here, we establish the sliced neocortical organoid (SNO) system, which bypasses the diffusion limit to prevent cell death and sustains neurogenesis in organized neural progenitor zones throughout long-term cultures. This method leads to the formation of an expanded cortical plate that establishes distinct upper and deep cortical layers, resembling the third-trimester human neocortex. Using the SNO system, we further identify a critical role of WNT/β-Catenin signaling in regulating cortical neuron fate specification, which is disrupted by a psychiatric disorder-associated genetic mutation in patient iPSC-derived organoids. These results demonstrate the utility of SNOs as a model for investigating previously inaccessible human-specific late-stage cortical developmental and disease-relevant mechanisms

overall_design: Profile transcriptome in day150 organoid in single cell level


title: RNA-Seq transcriptome profiling of postnatal age 35 days or P35 ventricles of cardiac-specific estrogen-related receptor alpha and gamma (ERRa/g) knock down (KD) mouse generated by AAV-cTnT-Cre injection and its control AAV-Luc injection.

status: Public on Jun 10 2020

first: Tomoya

last: Sakamoto

address: Smilow Center for Translational Research 11th FL (Room 11-172) 3400 Civic Center Blvd Bldg 421

department: Cardiovascular Institute

summary: Transcriptional regulatory circuits that drive cardiomyocyte maturation during the developmental process are poorly understood. Estrogen-related receptor alpha and gamma (ERRa/g) have been shown to be involved in all aspects of mitochondrial energy production. However, the function of ERR during the postnatal cardiac developmental process is unclear. To examine the role of (ERRa/g) during postnatal cardiac maturation, we generated inducible cardiac-specific ERRa/g knockdown (KD) mice with adeno-associated virus serotype 9 (AAV9) expressing Cre. We found that at P35 a number of genes involved in oxidative mitochondrial metabolism including OXPHOS, TCA cycle,  branched chain amino acid catabolism, and fatty acid oxidation were dramatically downregulated. Also, the KD hearts exhibited a significant downregulation of adult cardiac contractile protein, ion channel and Ca2+ handling genes. In contrast, fetal cardiac genes and non-cardiac genes that express in fibroblast or skeletal muscle cells were ectopically induced in the KD hearts. These results suggest that ERRa/g are essential factors for the broad postnatal cardiomyocyte maturation program.

overall_design: Examination of how gene expression levels are changed by KD ERRa/g during postnatal cardiac development in four replicates.

first: Shibiao

last: Wan

first: Daniel

middle: P

last: Kelly


title: Deep learning enables accurate clustering with batch effect removal in single-cell RNA-seq analysis

status: Public on Mar 21 2020

city: New York

first: Muredach

last: Reilly

address: 630 West 168th Street

department: Department of Medicine

institute: Columbia University Medical Center

summary: The data was used to evaluate the performance of single cell RNA-Seq clustering methods.

overall_design: The data was generated from human peripheral blood mononuclear clear cells by Ficoll Separation followed by CD14 and CD16 positive cell selection.

first: Huize

last: Pan


title: MUC1-C ACTIVATES THE NURD COMPLEX IN DEDIFFERENTIATION OF TRIPLE-NEGATIVE BREASTCANCER CELLS

city: Buffalo

first: Qiang

last: Hu

state: NY

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

summary: The NuRD chromatin remodeling and deacetylation complex, which includes MTA1, MBD3, CHD4 and HDAC1 among other components, is of importance for development and cancer progression. The oncogenic MUC1-C protein activates EZH2 and BMI1 in the epigenetic reprogramming of triple-negative breast cancer (TNBC) cells. However, there is no known link between MUC1-C and chromatin remodeling complexes. The present studies demonstrate that MUC1-C binds directly to the MYC HLH/LZ domain. In turn, we identified a previously unrecognized MUC1-C®MYC pathway that regulates the NuRD complex. We show that MUC1-C/MYC complexes selectively activate the MTA1 and MBD3 genes and posttranscriptionally induce CHD4 expression in basal- and not luminal-type BC cells. The results further show that MUC1-C forms complexes with these NuRD components on the ESR1 promoter. In this way, silencing MUC1-C (i) decreased MTA1/MBD3/CHD4/HDAC1 occupancy and increased H3K27 acetylation on the ESR1 promoter, and (ii) induced ESR1 expression and downstream estrogen response pathways. We also demonstrate that targeting MUC1-C and these NuRD components induces expression of FOXA1, GATA3 and other markers associated with the luminal phenotype. These findings and results from gain-of-function studies support a model in which MUC1-C activates the NuRD complex in driving luminal®basal dedifferentiation and plasticity of TNBC cells.

overall_design: BT-549 and SUM149 cells were transfected to stably express a control shRNA (CshRNA) or a MUC1shRNA. Total RNA was isolated from three different sets of the (i) BT-549/CshRNA and BT-549/MUC1shRNA cells, and (ii) SUM149/CshRNA and SUM149/MUC1shRNA cells. The RNA was used for RNA-seq library preparation.

first: H

last: Rajabi

first: D

last: Kufe


title: Epigenome analysis of normal ductal breast samples and infiltrating ductal breast cancer (BC) classified by tumour subtype

status: Public on Feb 17 2020

city: Pamplona

first: David

last: Guerrero-Setas

state: Navarra

address: C/ Irunlarrea, 3

department: Department of Pathology

country: Spain

institute: Complejo Hospitalario de Navarra

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of non-tumoral and infiltrating ductal breast cancer (tumoral) samples. The HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across approximately 450,000 CpG in non-tumoral and tumoral samples. Non-tumoral samples included six frozen non-neoplastic breast tissues from reduction mammoplasties and tumoral samples included eight frozen tumors from each BC subtype, i.e. luminal A (LA), luminal B (LB), luminal-HER2 (LH), HER2 (H) and triple-negative (TN) (Total: 40 tumors).

overall_design: Bisulphite converted DNA from the 46 samples were hybridised to the Infinium® HumanMethylation450 BeadChip


title: A Comprehensive Molecular Portrait of Human Urine-derived Renal Progenitor Cells

status: Public on Feb 03 2020

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

summary: Human urine is now recognized as a non-invasive source of stem cells with regeneration potential. These cells are mesenchymal stem cells but their detailed molecular and cellular identities are poorly defined. Furthermore, unlike the mouse, the gene regulatory network driving stemness and differentiation into functional renal cells in vitro remain unresolved. In this study, we isolated urine mesenchymal stem cells from 10 individuals of both genders and distinct ages, these cells express pluripotency- associated proteins- TRA-1-160, TRA-1-181, SSEA4, C-KIT and CD133. Expression of pluripotency-associated proteins enabled rapid reprogramming into iPSCs using episomal-based plasmids without pathway purtabations. Transcriptome analysis revealed expression of a plethora of nephrogenesis-related genes such as SIX2, OSR1, CITED1, NPHS2, NPHS1, PAX2, SALL1, AQP2, EYA1, SLC12A1 and UMOD. As expected the cells transport Albumin by endocytosis. Based on this we refer to these cells as urine derived renal progenitor cells- UdRPCs. Associated GO-term analysis of UdRPCs and UdRPC-iPSCs underlined their renal identity and functionality. Upon differentiation by WNT activation using the GSK3β inhibitor (CHIR99021), transcriptome and KEGG pathway analysis revealed upregulation of WNT-associated genes-AXIN2, JUN and NKD1. Protein interaction network identified JUN,- a downstream target of the WNT pathway in association with STAT3, ATF2 and MAPK1 as a putative key regulator of self-renewal and differentiation in UdRPCs. Furthermore, like pluripotent stem cells, self-renewal is maintained by FGF2-driven TGFβ-SMAD2/3 pathway. Ultimately, our in vitro model and the data presented in this study should lay the foundation for studying nephrogenesis in man.

overall_design: The transcriptomes of human UdRPCs were compared to human renal epithelial proximal cells and to UdRPCs treated with CHIR99021 as well as iPSCs derived from UdRPCs to human pluripotent cells (H1, H9, B4) by microarray analysis (PrimeView Human Gene Expression Array, Affymetrix, Thermo Fisher Scientific).

first: Lucas-Sebastian

last: Spitzhorn

first: S

last: Rahman

first: Martina

last: Bohndorf

first: Soraia

last: Martins

first: Nina

last: Graffmann

first: Audrey

last: Ncube

first: Fatima

last: Asar

first: James

last: Adjaye


title: Liver high-throughput sequencing of high-fat C57BL/6J wild-type mice

status: Public on Feb 18 2020

city: Shijiazhuang

first: Linyi

last: Shu

state: Hebei

address: 348 Heping West Road

department: Department of Endocrinology

country: China

institute: Hebei General Hospital

summary: Eight weeks after C57BL / 6J mice fed a high-fat diet (HFD), the degree of insulin resistance was assessed by intraperitoneal glucose tolerance test (IPGTT) and the insulin resistance model was successfully established. Mice were then treated with resveratrol and metformin for 6 weeks and blood and liver tissue samples were collected. Blood biochemical parameters were determined by kit, protein expression of hepatic insulin signaling pathway mRNA and mRNA was determined by Western blot and real-time polymerase chain reaction, and histomorphological changes were observed by histological staining. Mouse liver tissue samples were detected by high-throughput sequencing technology to obtain differential lncRNA expression profiles. Further differentially expressed genes were analyzed using bioinformatics techniques.

overall_design: Mice were divided into 4 groups, the livers were removed, snap frozen on dry ice, and RNA was harvested using Trizol reagent. Clusters were generated by cBot, diluted to a 10 pM library, and then sequenced on an Illumina NovaSeq 6000 (Illumina, USA).


title: m6A methylation regulates the fate of endogenous retrovirus transcripts

first: teissandier

last: aurelie


title: The long noncoding RNAs and mRNAs in the hepatocellular carcinoma at early and intermediate stage

status: Public on Jan 18 2020

city: Nanning

first: Xuefeng

last: Guo

state: Guangxi Zhuang Autonomous Region

address: 22 Shuangyong Road

department: 1.	Department of Epidemiology and Health Statistics

institute: Xuefeng Guo

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Recently, long noncoding rnas (lncRNAs) have been shown to have key roles in the development and prgression of hepatocellular carcinoma (HCC). However, the mechanism that contributes to the HCC biology is unknown, especially at the early and middle stages. In this study, we comprehensively investigaged lnRNAs and mRNAs expression in HCC.  We found three significant lnRNAs for diagostic markers in HCC at early stage.

overall_design: A ten chip study using total RNA recovered from five HCC tissues and corresponding five HCC adjacent normal tissues

first: Guo

middle: X

last: Feng

first: Qiu

last: Qiang


title: Nutrient regulation of liver gene expression

city: Bronx

first: Jeffrey

middle: E

last: Pessin

address: 1301 Morris Park Avenue

department: Medicine and Molecular Pharmacology

institute: Albert Einstein College of Medicine

summary: We have obtained RNAseq data from the livers of male C57BL/6J and BALB/c that were maintained on a low-fat (10 kcal%fat) diet (PicoLab Mouse Diet 5053) and then fasted overnight or following fasting fed with low-fat diet supplemented with or without 20% glucose, fructose or sucrose in their drinking water for 3, 6 and 12 h. Out of 130 mice, we have successfully obtained 128 liver mRNAseq datasets that are currently being analyzed for differences in specific gene expression, the extent of gene expression and the inter-strain variability among replicates for each gene in each strain and under each dietary condition. We have observed distinct expression differences in terms of the time course and magnitude of gene expression changes between these two strains of mice. These differences also are dependent upon the specific carbohydrate present in each diet.

overall_design: Male mice at 8 weeks of age were purchased from the Jackson Laboratory and trained for 1 week for a well timed fasting and feeding protocol. On the last day of training, after fasting for 21 h, mice were sacrificed at 0, 3, 6 and 12 h following feeding and their livers were isolated and snap frozen in liquid N2. Total RNA was extracted. RNAseq ~ 30 million reads, 150 bp pair-ended were obtained.

first: Yuling

last: Chi

first: Li

last: Liu


title: Epigenetic remodelling of enhancers in response to estrogen deprivation and re-stimulation

status: Public on Jan 01 2020

city: Lyon

first: Zdenko

last: Herceg

address: 25 avenue Tony Garnier CS 90627

department: EGM

institute: IARC


title: Dynamics of transcriptomes of hPSCs treated by CHIR99021 for 21 hours

status: Public on Dec 25 2019

city: University park

first: Yuqian

last: Jiang

address: W345 millennium science complex

institute: PSU

summary: We have evidence to demonstrate that hPSCs enter mesoderm or endoderm lineages dependent on the dose of WNT signaling activation. To understand the underlying mechanism of CHIR99021-induced definitive endoderm (DE) differentiation, we collected hPSCs treated by CHIR99021 for 21 hours and performed RNA sequencing, to investigate the dynamics of transcriptomes in every three hours post CH treatment.

overall_design: 19-9-11 hiPSCs were treated with 6 uM CHIR99021 in RPMI medium and cells were collected for RNA sequencing for every three hours until 21h.

first: Xiaojun

last: Lian


title: m6A methylation regulates the fate of endogenous retrovirus transcripts [CRISPR/Cas9]

overall_design: Genome-wide loss-off-function CRISPR/Cas9 knock out screen using mouse embryonic stem cells carrying IAPEz transposon reporter cassette.

first: Tomasz

last: Chelmicki

first: Aurelie

last: Teissandier


title: Epigenetic remodelling of enhancers in response to estrogen deprivation and re-stimulation [methylArray]

summary: Estrogen hormones are implicated in a majority of breast cancers and estrogen receptor alpha (ER) orchestrates a complex molecular circuitry that is not yet fully elucidated. Here we investigated genome-wide DNA methylation, histone acetylation and transcription after estradiol (E2) deprivation and re-stimulation to better characterise the ability of ER to coordinate gene regulation. We found that E2 deprivation mostly resulted in DNA hypermethylation and histone deacetylation in enhancers. Transcriptome analysis revealed that E2 deprivation leads to a global down-regulation in gene expression. Enrichment analysis of transcription factor (TF) binding and motif occurrence in the proximity of E2 deprivation-mediated differentially methylated and acetylated sites reinforces the importance of AP-1 and FOX proteins, Finally, most deprivation-dependent epigenetic changes were reversed following E2 re-stimulation.

overall_design: Control MCF-7 HTB-22 breast cancer cells (CTR) were cultured continuously for 14 days in E2-containing medium, while E2-deprived cells (E2D) were cultured in the same conditions as CTR only lacking E2. The re-stimulated cells (ReSt) were E2-deprived for 4 days and re-stimulated for the 10 following. Each treatment (CTR, E2D and ReSt) and time point (d0, d4, d14) is available in triplicates. See publication for schematic design

first: Athena

last: Sklias


title: Epigenetic remodelling of enhancers in response to estrogen deprivation and re-stimulation [ChIP-Seq]

overall_design: Control MCF-7 HTB-22 breast cancer cells (CTR) were cultured continuously for 14 days in E2-containing medium, while E2-deprived cells (E2D) were cultured in the same conditions as CTR only lacking E2. The re-stimulated cells (ReSt) were E2-deprived for 4 days and re-stimulated for the 10 following. Each treatment (CTR, E2D and ReSt) and timepoint (d0, d4, d14) is available in triplicates. See publication for schematic design


title: Methylation data from radiation-induced glioma and reference cohort

status: Public on Dec 24 2019

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

summary:
Long-term complications such as radiation-induced second malignancies occur in a subset of patient following radiation-therapy, particularly relevant in pediatric patients due to the long follow-up period in case of survival. Radiation-induced gliomas (RIGs) have been reported in patients after treatment with cranial irradiation for various primary malignancies such as acute lymphoblastic leukemia (ALL) and medulloblastoma (MB).
Our study revealed a unifying molecular signature for the majority of RIGs, with recurrent PDGFRA amplification and loss of CDKN2A/B and an absence of somatic hotspot mutations in genes encoding histone 3 variants or IDH1/2, uncovering diagnostic markers and potentially actionable targets.

overall_design: We performed comprehensive (epi-) genetic and expression profiling of RIGs arising after cranial irradiation for MB (n=25) and ALL (n=8) with reference cohorts representing other pediatric brain tumor entities.

first: Maximilian

middle: Y

last: Deng

first: Dominik

last: Sturm

first: Elke

last: Pfaff

first: Gnana

last: Balasubramian

first: Stephan

last: Tippelt

first: Christof

last: Kramm

first: Andrew

last: Donson

first: Adam

middle: L

last: Green

first: Chris

last: Jones

first: Jens

last: Schittenhelm

last: Ebinger

middle: U

last: Schuhmann

first: Barbara

last: Worst

first: Cornelis

last: van Tilburg

first: Andrea

last: Wittmann

first: Martina

last: Ryzhova

first: Jonas

last: Ecker

first: Till

last: Milde

first: Olaf

last: Witt

first: Felix

last: Sahm

first: David

last: Reuss

last: Sumerauer

first: Josef

last: Zamecnik

first: Andrey

last: Korshunov

first: Andreas

last: von Deimling

first: Stefan

last: Pfister

middle: T


title: The DNA Methylation patterns of ART and naturally conceived pregnancies

city: Beijing

first: zhang

middle: zi

last: long

address: NO.1 Beichen West Road

institute: Beijing Institute of Genomics

summary: Genome wide DNA methylation profiling of normal and ART newborn. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs. Samples included 6 normal newborn heelblood, 6 ART newborn heelblood.

overall_design: Examination of DNA methylation in 6 ART-conceived pregnancies and 6 naturally conceived pregnancies using the Infinium HumanMethylation 450k Beadchip.

first: Zilong

last: Zhang

first: Zongzhi

last: Liu


title: m6A methylation regulates the fate of endogenous retrovirus transcripts [RNA-seq]

first: teissandier

last: aurelie

address: 26 rue d'Ulm

summary: Using a genome-scale CRISPR knockout screening in mouse embryonic stem cells, we identify m6A RNA methylation as an important regulatory component that restricts the activity of endogenous retroviruses of the IAP (intracisternal A-particles) family. The m6A methylation of IAP mRNAs occurs on their 5’ end, is catalyzed by the complex of methyltransferase-like (METTL)3/METTL14 proteins whose depletion, along with other complex subunits, namely WTAP and ZC3H13, leads to increased IAP transcript abundance. Using auxin-dependent degron, we show that rapid removal of METTL3, METTL14 and ZC3H13 further increases IAP RNA abundance in a progressive and reversible fashion. Finally, we demonstrate that m6A RNA reduces the stability of IAP transcripts

overall_design: Comparison of RNA-seq samples from mouse embryonic stem cells (ESCs) for WT, Mettl3-/-, Mettl14-/-, Wtap-/- and Zc3h13-/- conditions

first: Tomasz

last: Chelmicki

first: Aurelie

last: Teissandier


title: Epigenetic remodelling of enhancers in response to estrogen deprivation and re-stimulation [RNA-Seq]

first: Zdenko

last: Herceg

first: Athena

last: Sklias

first: Rabih

last: Murr


title: Epigenomics and transcriptome analysis of ESCC

status: Public on Dec 20 2019

city: Shantou

first: Yang

last: Chen

address: Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou

institute: Shantou University Medical College

type:
Expression profiling by array
Methylation profiling by array

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: RNA-seq of UGP2 mutant human embryonic stem cells and in vitro differentiated neural stem cells

status: Public on Dec 10 2019

city: Rotterdam

first: Tahsin Stefan

last: Barakat

state: South Holland

address: Dr. Molewaterplein 40

department: Clinical Genetics

country: Netherlands

institute: The Erasmus University Medical Center

summary: We report transcriptome analysis of human embryonic stem cells  and in vitro differentiated neural stem cells, comparing wild type H9, UGP2 homozygous knock-out and UGP2 mutant cells harboring a homozygous A>G  nucleotide change affecting the start codon of UGP2 isoform 2 that was introduced by CRISPR-Cas9 engineering

overall_design: For the RNA-seq experiments, two independent H9 wild type cultures, two independent knock-out clones harboring the same homozygous genetic alteration in UGP2 and two independent clones harboring the  homozygous UGP2 mutation were used. All 6 cell lines (two biological replicates per genotype) were cultured in two technical replicates, and sequenced at the hESC state and as NSCs cultured at passage 5 upon NSC differentiation.

first: Tahsin

middle: S


title: Expression of E93 provides an instructive cue to control dynamic enhancer activity and chromatin accessibility during development

status: Public on Feb 25 2020

city: Chapel Hill

first: Spencer

last: Nystrom

state: NC

address: 250 Bell Tower Drive

department: Curriculum in Genetics and Molecular Biology

institute: UNC-Chapel Hill

summary: How temporal cues combine with spatial inputs to control gene expression during development is poorly understood. Here, we test the hypothesis that the Drosophila transcription factor E93 controls temporal gene expression by regulating chromatin accessibility. Precocious expression of E93 early in wing development reveals that it can simultaneously activate and deactivate different target enhancers. Notably, the precocious patterns of enhancer activity resemble the wild-type patterns that occur later in development, suggesting that provision of E93 alters the competence of enhancers to respond to spatial cues. Genomic profiling reveals that precocious E93 expression is sufficient to regulate chromatin accessibility at a subset of its targets. These accessibility changes mimic those that normally occur later in development, indicating that precocious E93 accelerates the wild-type developmental program. Further, we find that target enhancers that do not respond to precocious E93 in early wings become responsive after a developmental transition, suggesting that parallel temporal pathways work alongside E93. These findings support a model wherein E93 expression functions as an instructive cue that defines a broad window of developmental time through control of chromatin accessibility.

overall_design:
FAIRE-seq from Drosophila 3LW wings precociously expressing HA-tagged E93 under control of a wing-specific driver (labeled "E93GOF" below). ChIP-seq against precociously expressed HA-tagged E93 in third-instar wandering (3LW) wing discs; includes a negative control ChIP experiment from wing discs containing the GAL4 driver but not the UAS-E93-3xHA transgene (labeled "VgControl" below). We compare these data to a developmental timecourse of chromatin accessibility as measured by FAIRE-seq in wild-type and E93-mutant wing discs and ChIP-seq for a GFSTF-tagged allele of E93 in otherwise wild-type 24hAPF pupal wings.

This series includes re-analyzed samples from: GSE38727, GSE97956 and GSE131981.

first: Matthew

middle: J

last: Niederhuber

first: Daniel

last: McKay


title: RNA isoform screens reveal the essentiality and tumor suppressor activity of ultraconserved poison exons

status: Public on Nov 19 2019

city: Seattle

first: James

middle: Douglas

last: Thomas

state: WA

address: 1100 Fairview Ave. N., B3-111

department: Computational Biology

institute: Fred Hutchinson Cancer Research Center

summary: Paired gRNA/Cas9 delivery facilitates the removal of alternative exons and reveals splicing dependent phenotypes.

overall_design: RNA-seq of HeLa/iCas9 and PC9-Cas9 cells treated with pgRNA vectors. Untreated controls (HeLa and PC9) are also included.

middle: D

first: Robert

middle: K

last: Bradley


title: Analysis of gene expression, motif and pattern of m6A modified region and m6A enrichment level in Ocular melanoma and Melanocyte cell lines. Gene expressin analysis of METTL3 knock down in PIG1, ALKBH5 knock down and HINT2 over expression in OCM1.

status: Public on Nov 25 2019

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

summary: Dynamic N6-methyladenosine (m6A) RNA modification installed and erased by N6-methyltransferases and demethylases regulates gene expression, alternative splicing and cell fate. Ocular melanoma, comprising uveal melanoma (UM) and conjunctival melanoma (CM), is the most common primary eye tumor in adults and the 2nd most common melanoma. However, the functional role of m6A modification in ocular melanoma remains unclear. Here, we show that RNA methylation significantly inhibits the progression of uveal melanoma and conjunctival melanoma. Ocular melanoma samples showed decreased m6A levels, indicating a poor prognosis. Changes in global m6A modification were highly associated with tumor progression in vitro and in vivo. Mechanistically, YTHDF1 promoted the translation of methylated HINT2 mRNA, a tumor suppressor in ocular melanoma. Our work uncovers a critical function for m6A methylation in ocular melanoma and provides additional insight into the understanding of m6A modification.

overall_design: RNA-seq, miCLIP-seq and MeRIP-seq for five Ocular melanoma cell lines (CM2005.1, CRMM1, OCM1, OCM1a and OM431) and one Melanocyte cell line (PIG1).

first: Ruobing

last: Jia

first: Peiwei

last: Chai

first: Shanzheng

last: Wang

first: Baofa

first: Yangfan

last: Xu

first: Ying

last: Yang

first: Shengfang

last: Ge

first: Renbing

first: Yun-Gui

first: Xianqun

last: Fan


title: Subcellular pathways shared by afflicted patients and mutant mice identify a new drug treatment for aortic aneurysm in Marfan syndrome

status: Public on Nov 18 2019

city: PARIS

first: Pauline

last: ARNAUD

address: 46, rue Henri Huchard

institute: AP-HP - Hôpital Bichat

summary: We analyzed differentially expressed genes in smooth muscle cells derived from the thoracic aorta of Marfan Syndrome (MFS) patients and control subjects to identify cell biological mechanisms contributing to thoracic aoritc aneurysm (TAA) development and rupture. These mechanisms were used to identify a potential drug treatment to mitigate TAA progression. We analyzed differentially expressed genes in whole aorta of P16 MFS mice vs WT mice to identify cell biological mechanisms contributing to thoracic aoritc aneurysm (TAA) development and rupture. These mechanisms were used to identify baclofen as a potential drug treatment to mitigate TAA progression. The effect of baclofen on gene expression in WT and MFS was documented in P60 mice that received treatment since P16.

overall_design: Identification of differentially expressed genes in smooth muslce cells derived from the aorta of Marfan Syndrome patients. Identification of differentially expressed genes in thoracic aortic wall of MFS vs WT mice and of baclofen treated MFS/WT mice vs untreated MFS WT mice.

first: Jens

last: Hansen

first: Josephine

last: Galatioto

first: Cristina

middle: I

last: Caescu

last: Arnaud

first: Rhodora

last: Calizo

first: Bart

last: Spronch

first: Sae-II

last: Murtada

first: Roshan

last: Borkar

first: Evren

last: Azeloglu

first: Maria

last: Bintanel-Morcillo

last: Gallo

first: Jay

last: Humphrey

first: Guillaume

last: Hondeau

first: Catherine

last: Boileau

first: Francesco

last: Ramirez

first: Ravi

last: Iyengar


title: RNA-sequence facilitates analyze changes of signaling pathways after drug treatment

status: Public on Oct 29 2019

city: Nanjing

first: Qing

last: Liu

address: No. 12 Xuefu Road, Pukou District

institute: Model Animal Research Center, Nanjing University

summary: Mammalian cochlear hair cells cannot regenerate after damage, which was a cause of hearing loss. Due to the small number of cochlear hair cells, we were unable to collect enough cells for research. Therefore, we have established a inner ear organoid model in this way, which greatly expands the number of supporting cells, Lgr5 and gradually mature hair cells. It can be used in high-throughput screening experiments. Using this model for high-throughput screening of FDA small molecule Drug, we found that Regorafenib can promote hair cell regeneration in vitro and get more mature regenerated hair cells. And we found that Regorfenib was though a new VEGF-TGFB axis to regulate hair cell regeneration.

overall_design: Compare these changes in these signal pathways after drug treatment

first: Linqing

last: Zhang


title: Single-cell transcriptome analysis of uniparental embryos reveals parent-of-origin effects on human preimplantation development [RNA-seq]

status: Public on Oct 08 2019

city: Changsha

first: leng

last: lizhi

address: xiangya road

institute: Central South University

summary: To investigate the contribution of parental genomes to early embryogenesis, we systematically profiled the single-cell transcriptomes of human biparental and uniparental embryos from one-cell to morula stages. We observed that uniparental embryos exhibit variable and overall less activation patterns of embryonic genome activation (EGA). Comparative transcriptome analysis identified 807 maternally biased expressed genes (MBGs) and 581 paternally biased expressed genes (PBGs) in preimplantation stages. MBGs became obviously appeared at the four-cell stage and contribute to EGA initiation, whereas PBGs preferentially appeared at the eight-cell stage, and possibly affect embryo compaction and trophectoderm specification. Regulatory network analysis revealed DUX4, EGR2 and DUXA as key transcription factors for MBGs expression as well as ZNF263 and KLF3 for PBGs expression. Furthermore, we revealed that the expression of MBGs and PBGs especially PBGs, probably due to DNA methylation differences between the parental genomes. Together, our results provide a valuable resource to understand parental genome activation and may help to dissect parent-of-origin effect on early human development.

overall_design:
We performed a comprehensively survey of transcriptional activities between biparental and uniparental embryos by single-cell RNA sequencing
BI: biparental, AG: androgenetic, PG: parthenogenetic

first: Lizhi

last: Leng

first: Ge

last: Lin


title: Global Transcriptome Characterization and Assembly of thermophilic ascomycete Chaetomium thermophilum

status: Public on Dec 31 2019

first: Ed

last: Hurt

address: Im Neuenheimer Feld 328

department: BZH

institute: Biochemie Zentrum Heidelberg

summary:
A correct genome annotation is fundamental for research in the field of molecular and structural biology.
The annotation of the reference genome of Chaetomium thermophilum has been reported previously, but it is limited to open reading frames (ORFs) of genes and contains only a few noncoding transcripts.
In this study, we identified and annotated by deep RNA sequencing full-length transcripts of C.thermophilum. We identified 7044 coding genes and a large number of noncoding genes (n=4567).
Astonishingly, 23% of the coding genes are alternatively spliced. We identified 679 novel coding genes and corrected the structural organization of more than 50% of the previously annotated genes.
Furthermore, we substantially extended the Gene Ontology (GO) and Enzyme Commission (EC) lists, which provide comprehensive search tools for potential industrial applications and basic research.
The identified novel transcripts and improved annotation will help understanding the gene regulatory landscape in C.thermophilum.
The analysis pipeline developed here can be used to build transcriptome assemblies and identify coding and noncoding RNAs of other species.
The new genome annotation of the GTF file can be found here.

overall_design: Poly-A RNA-seq on Chaetomium thermophilum, with 3 replicates

first: Amit

last: Singh

first: Géza

last: Schermann

first: Sven

last: Reislöhner

first: Nikola

last: Kellner

first: Michael

last: Bruner


title: Single-cell transcriptome analysis of uniparental embryos reveals parent-of-origin effects on human preimplantation development

type: Methylation profiling by high throughput sequencing


title: Single-cell transcriptome analysis of uniparental embryos reveals parent-of-origin effects on human preimplantation development [methylation]

summary: To investigate the contribution of parental genomes to early embryogenesis, we systematically profiled the single-cell transcriptomes of human biparental and uniparental embryos from one-cell to morula stages. We observed that uniparental embryos exhibit variable and overall less activation patterns of embryonic genome activation (EGA). Comparative transcriptome analysis identified 807 maternally biased expressed genes (MBGs) and 581 paternally biased expressed genes (PBGs) in preimplantation stages. MBGs became obviously appeared at the four-cell stage and contribute to EGA initiation, whereas PBGs preferentially appeared at the eight-cell stage, and possibly affect embryo compaction and trophectoderm specification. Regulatory network analysis revealed DUX4, EGR2 and DUXA as key transcription factors for MBGs expression as well as ZNF263 and KLF3 for PBGs expression. Furthermore, we revealed that the expression of MBGs and PBGs，especially PBGs, probably due to DNA methylation differences between the parental genomes. Together, our results provide a valuable resource to understand parental genome activation and may help to dissect parent-of-origin effect on early human development.

overall_design:
We performed a comprehensively survey of methylation levels between biparental and uniparental embryos by single embryo whole genome bisulfite-seq.
BI: biparental, AG: androgenetic, PG: parthenogenetic

first: Jinrong

last: Huang


title: TGFβ signaling in retinal tissue repair [Danio Rerio]

status: Public on Nov 03 2019

city: Bern

first: Federica Maria

last: Conedera

state: Bern

address: Freiburgstrasse 14

country: Switzerland

institute: Inselspital-University of Bern

summary: In mammals, retinal damage is followed by Müller glia cell activation and proliferation. While retinal gliosis persists in adult mammals after an insult or disease, some vertebrates, including zebrafish, have the capacity to regenerate. We believe we are the first group to show that gliosis is a fibrotic-like process in mammals’ eyes caused by differential activation of canonical and non-canonical TGFβ signaling pathways.

overall_design: Comparison of murine and fish Müller cell transcriptome post retinal injury

first: Federica

middle: M

first: Ana

last: Pousa

first: David

last: Presby

first: Nadia

last: Mercader

first: Volker

last: Enzmann

first: Markus

last: Tschopp


title: Generating in vivo somatic mouse mosaics with locus-specific, stably-integrated transgenic elements for studies of gene function in development and tumorigenesis [bulk ATAC-seq]

status: Public on Sep 10 2019

city: West Hollywood

first: AGCT

last: Core

state: CA

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

summary: We report the development and efficiency of a new method to create somatic mosaicism in mice named as mosaic analysis by dual recombinase-mediated cassette exchange. Then we generate, as a proof of concept, a new model for pediatric glioma.

overall_design: Examination by ATAC-seq of a PiggyBack-based mouse model for pediatric brain tumors as compared with normal healthy mouse brain and with the MADR model data at single-cell ATACseq and single-cell RNAseq levels.

first: Gi

middle: B

last: Kim

last: Rincon-Fernandez-Pacheco

last: Saxon

first: Amy

last: Yang

first: Sara

last: Sabet

first: Marina

last: Dutra-Clarke

first: Rachelle

last: Levy

first: Ashley

last: Watkins

first: Hannah

last: Park

first: Aslam

middle: A

last: Akhtar

first: Paul

last: Linesch

first: Naomi

last: Kobritz

first: Shea

last: Chandra

first: Jessica

last: Molina

first: Daniel

last: Gareau

first: Kendy

last: Hoang

first: Jerimiah

last: Tsyporin

first: Serguei

last: Bannykh

first: Chintda

last: Santiskulvong

first: Yizhou

last: Wang

first: Jie

last: Tang

first: Mario

last: Suva

first: Bin

last: Chen

first: Moise

last: Danielpour

first: Joshua

last: Breunig


title: Genome-wide DNA methylation sequencing in C2C12 myoblasts and myotubes

status: Public on Nov 27 2019

city: Kunming

first: Chao

last: Zhang

state: Yunnan

address: No.17 Longxin Road

department: Kunming Institute of Zoology

institute: Chinese Academy of Sciences

summary: We show the application of 5mC antibody-based methylated DNA immunoprecipitation followed sequencing technology for high-through profiling of DNA methylation in mouse C2C12 myoblasts and myotubes. By analyzing the methylation status of immunoprecipitated DNA fragments, we generated genome-wide DNA methyaltion maps in mouse C2C12 myoblasts and myotubes. We find that DNA methylation levels in myoblasts at rDNA promter and coding regions are higher than that in myotubes but not changed in intergenic regions.

overall_design: We test the DNA methylation status in undifferentiated myoblasts and myotubes differentiated with the 2% horse serum for 6 days by utilizing the MeDIP seq technology.

first: Wei

last: Tao

first: Le

last: Zong


title: TGFβ signaling in retinal tissue repair [Mus Musculus]

first: Federica Maria

last: Conedera

first: Federica

first: Ana

last: Pousa

first: David

last: Presby

first: Nadia

last: Mercader

first: Volker

last: Enzmann

first: Markus

last: Tschopp


status: Public on Nov 26 2019

city: Richardson

first: Theodore

middle: John

last: Price

state: TX

address: 800 W Campbell Rd

department: Behavioral and Brain Sciences

institute: The University of Texas at Dallas

summary:
Dorsal root ganglion (DRG) neurons detect sensory inputs and are crucial for pain processing. They are often studied in vitro as dissociated cell cultures with the assumption that this reasonably represents in vivo conditions. However, to our knowledge, no study has directly compared genome-wide transcriptomes of DRG tissue in vivo versus in vitro, or between laboratories and culturing protocols. Comparing RNA sequencing-based transcriptomes of native to cultured (4 days in vitro) human or mouse DRG, we found that the overall expression levels of many ion channels and GPCRs specifically expressed in neurons are markedly lower although still expressed in culture.  This suggests that most pharmacological targets expressed in vivo are present under the condition of dissociated cell culture, but with changes in expression levels. The reduced relative expression for neuronal genes in human DRG cultures is likely accounted for by increased expression of genes in fibroblast-like and other proliferating cells, consistent with their mitotic status in these cultures. We found that the expression of a subset of genes typically expressed in neurons increased in human and mouse DRG cultures relative to the intact ganglion, including genes associated with nerve injury or inflammation in preclinical models such as BDNF, MMP9, GAL, and ATF3.  We also found a striking upregulation of a number of inflammation-associated genes in DRG cultures, although many were different between mouse and human.  Our findings suggest an injury-like phenotype in DRG cultures that has important implications for the use of this model system for pain drug discovery.
Related datasets : Human datasets are present in the dbGaP study id phs001158.v3.p1 . Use the sample attribute "Project id" to determine which samples In that were used for thie project "Pharmacological target focused transcriptomic analysis of native versus cultured human and mouse dorsal root ganglia"

overall_design: Acutely dissected and cultured DRGs were profiled using RNA-seq in mice from two separate laboratories with differing culturing protocols. Differences between laboratories, between acutely dissected and cultured samples, and between mouse and similarly cultured human datasets were analyzed

first: Pradipta

middle: R

last: Ray

first: Nizar

last: Ghneim

first: Andi

last: Wangzhou

first: Lisa

last: McIlvried

first: Candler

last: Paige

first: Paulino

last: Barragan-Iglesias

first: Stephanie

last: Shiers

first: Ayesha

last: Ahmad

first: Carolyn

last: Guzman

first: Gregory

last: Dussor

first: Robert

middle: W

last: Gereau


title: Generating in vivo somatic mouse mosaics with locus-specific, stably-integrated transgenic elements for studies of gene function in development and tumorigenesis [ChIP-seq]

first: AGCT

last: Core

summary: We report the development and eficiency of a new method to create somatic mosaicism in mice named as mosaic analysis by dual recombinase-mediated cassette exchange. Then we generate, as a proof of concept, a new model for pediatric glioima

overall_design: Examination by Chip-seq of 3 mouse model pediatric brain tumors

first: Gi

last: Kim

last: Rincon-Fernandez-Pacheco

last: Saxon

first: Amy

last: Yang

first: Sara

last: Sabet

first: Marina

last: Dutra-Clarke

first: Rachelle

last: Levy

first: Ashley

last: Watkins

first: Hannah

last: Park

first: Aslam

last: Akhtar

first: Paul

last: Linesch

first: Naomi

last: Kobritz

first: Shea

last: Chandra

first: Jessica

last: Molina

first: Daniel

last: Gareau

first: Kendy

last: Hoang

first: Jerimiah

last: Tsyporin

first: Serguei

last: Bannykh

first: Chintda

last: Santiskulvong

first: Yizhou

last: Wang

first: Jie

last: Tang

first: Mario

last: Suva

first: Bin

last: Chen

first: Moise

last: Danielpour

first: Joshua

last: Breunig


title: Generating in vivo somatic mouse mosaics with locus-specific, stably-integrated transgenic elements for studies of gene function in development and tumorigenesis [scRNA-seq]

first: AGCT

last: Core

overall_design: Examination by scRNAseq of 3 mouse model pediatric brain tumors

first: Gi

last: Kim

first: David

last: Rincon-Fernandez-Pacheco

last: Saxon

first: Amy

last: Yang

first: Sara

last: Sabet

first: Marina

last: Dutra-Clarke

first: Rachelle

last: Levy

first: Ashley

last: Watkins

first: Hannah

last: Park


title: Generating in vivo somatic mouse mosaics with locus-specific, stably-integrated transgenic elements for studies of gene function in development and tumorigenesis


title: Stag2 regulates hematopoietic differentiation and self-renewal through alterations in gene expression and topological control

status: Public on Sep 02 2019

city: Worcester

first: Job

last: Dekker

address: 368 Plantation Street, AS5-1049

department: Program in Systems Biology

institute: University of Massachusetts Medical School

summary: We performed HiC analyzed on wildtype and Stag2 knock-out hematopoietic progeitor cells and integrated with Stag2 ChIP-seq and RNAseq data to identy genes whose expression and tological structures are regulated by Stag2 during hematopoietic differentiation and self-renewal.

overall_design: Comparing HiC profiles of two wildtype hematopoietic progenitor cells with two Stag2 KO cells.

first: Yu

last: Liu


title: Transcriptional profiling reveals an upregulation of genes related to Sphingolipid metabolism and Oxidative phosphorilation in HRas and NRas double-KO mice (DKO), which die because of a severe respiratory distress.

status: Public on Jul 15 2019

city: Salamanca

first: Eugenio

last: Santos

address: Campus Miguel de Unamuno

department: Instituto de Biología Celular y Molecular del Cáncer

institute: Universidad de Salamanca y CBERONC

summary: We used microarrays to investigate gene expression changes in the lungs of Control, Hras-KO, Nras-KO and DKO mice. These DKO animals die at birth because of respiratory distress, caused by an impaired lung maturation.

overall_design: Manually selected lungs of Control, HRas-KO, NRas-KO and DKO from postnatal day 0 were used for RNA extraction using the TRIZOL protocol. RNA was further purified using Qiagen Rneasy mini kit. Each RNA sample for each microarray was obtained from one individual animal.

first: R

last: Fuentes-Mateos

first: A

last: Fernandez-Medarde

first: E


title: The prevalence, evolution and chromatin signatures of plant regulatory elements

status: Public on Sep 19 2019

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: Chromatin accessibility and modification is a hallmark of regulatory DNA, which has led to the discovery of cis-regulatory elements (CREs). Here, we characterize chromatin accessibility, histone modifications and sequence conservation in 13 plant species. We identified thousands of putative CREs and revealed that distal CREs are prevalent in plants especially in species with large and complex genomes. The majority of distal CREs have been moved away from their target genes by transposable element (TE) proliferation, but a significant number of distal CREs also appear to be created by TEs. Finally, plant distal CREs are associated with three major types of chromatin signatures that are distinct from metazoans. Taken together, these results suggest that CREs are prevalent in plants, highly dynamic during evolution, and function with distinct chromatin pathways to regulate gene expression.

sample_organism:
Populus trichocarpa
Arabidopsis thaliana
Glycine max
Phaseolus vulgaris
Hordeum vulgare
Oryza sativa
Setaria viridis
Sorghum bicolor
Zea mays
Asparagus officinalis
Brachypodium distachyon
Spirodela polyrhiza
Eutrema salsugineum

overall_design: Examination of Chromatin accessibilities, different histone modifications, and expressions in 13 plant species.


title: RNA Sequencing to Identify Regulators of Axon Regeneration in Mouse Retinal Ganglion Cells

status: Public on May 29 2019

city: Miami

first: Kyung (Kevin)

state: FL

address: 1095 NW 14th Terrace, Miami Project to Cure Paralysis, LPLC room 4-20

department: Neurological Surgery

institute: University of Miami

summary:
Purpose: The goals of this study are to identify the transcriptional profile of retinal ganglion cells (RGCs) with the capacity to regenerate an axon, and contrast this profile with the profile of RGCs that cannot regenerate an axon.

Methods: See sample pages for protocols for tissue preparation, RNA extraction and purification, library construction and data processing.

Results: RNA from the 12 samples was sequenced to an average depth of 42 million reads. Genes were considered expressed if a gene had an expression of 1 count per million in 3 of the 12 samples. There were 13,406 genes that met this criterion.

Conclusions: Our study represents the first analysis by NGS of highly-purified RGCs in the context of axonal injury

overall_design: RGC mRNA profiles of melanopsin RGCs and ON-OFF Direction Selective Ganglion Cells (ooDSGCs) were generated by deep sequencing in triplicate, using Illumina HiSeq 2500.

first: Eric

last: Bray

first: Kevin


title: TGFβ signaling in retinal tissue repair

first: Federica Maria

last: Conedera

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design: Refer to individual Series


status: Public on May 14 2019

city: Ulm

first: Tamás

last: Röszer

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

institute: University of Ulm

summary:
AKGs enriched transcripts associated with PC-, lyso-PC and PAF metabolism. Moreover, AKGs suppressed interferon response genes.
We submit heren three sets of NGS analyses. Experiment 1: We treated mouse adipose tissue macrophages (ATMs) with vehicle (ethanol) or 100 nM alkylglycerols (AKGs) for 18h in vitro. Experiment 2: We treated mouse 3T3-L1 preadipocytes with 1 nM neuropeptide FF (NPFF) for 18 h. Experiment 3: we isolated white adipose tissue from C57Black/6 male mice at 8 weeks of age, and brown adipose tissue from the same mice.

overall_design: Experiment 1: 3 Vehicle-treated, and 3 AKG-treated samples. Experiment 2: 3 Vehicle-treated and 3 NPFF-treated samples. Experiment 3: 3 white adipose tissue (Bveh) and 3 brown adipose tissue (BAKG). In the latter case the sample naming refers to the project acronyms.


title: Differentially expressed genes after siRNA transfection in human cancer cell lines II

status: Public on Mar 30 2019

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

country: Japan

institute: Chiba University

summary: To identify differentially expressed genes by anti cancer treatments (miRNA and siRNAs) in human cancer, several cell lines (breast cancer, colorectal cancer and renal cancer) were subjected to Agilent whole genome microarrays.

overall_design: Human cell lines (HCT116, MDA-MB-231, 786-O and A498) were treated with miRNA (miR-139-5p, miR-139-3p, miR-490-5p and miR-490-3p) and siRNAs (si-GINS1).

first: Yasutaka

last: Yamada


title: Gene expression profiles with matched NGS in B-cell non-Hodgkin lymphoma

status: Public on Jun 19 2019

city: Houston

first: Michael

last: Green

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

institute: MD Anderson Cancer Center

summary: This series consists of gene expression microarray data from non-Hodgkin lymphoma tumors for which we have performed targeted DNA sequencing with the 380 gene LymphoSeq panel.

overall_design: RNA was extracted frin fresh/frozen tumor specimens and interrogated by Affymetrix U133 plus 2.0 microarray.


title: Stag1 and Stag2 regulate cell fate decisions in hematopoiesis through non-redundant topological control

status: Public on Sep 24 2019

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center


title: Generating in vivo somatic mouse mosaics with locus-specific, stably-integrated transgenic elements for studies of gene function in development and tumorigenesis [scATAC-seq]

first: AGCT

last: Core

overall_design: Examination by 10X single-cell ATAC-seq of 2 mouse model pediatric brain tumors.

first: Gi

last: Kim

first: David

last: Rincon-Fernandez-Pacheco

last: Saxon

first: Amy

last: Yang

first: Sara

last: Sabet

first: Marina

last: Dutra-Clarke

first: Rachelle

first: Ashley

first: Hannah

first: Aslam

last: Akhtar

first: Paul

last: Linesch

first: Naomi

last: Kobritz

first: Shea

last: Chandra

first: Jessica

last: Molina

first: Daniel

last: Gareau

first: Kendy

last: Hoang

first: Jerimiah

last: Tsyporin

first: Serguei

last: Bannykh

first: Chintda

last: Santiskulvong

first: Yizhou

last: Wang

first: Jie

last: Tang

first: Mario

last: Suva

first: Bin

last: Chen

first: Moise

last: Danielpour

first: Joshua

last: Breunig


title: Adrenal gland gene expression in male pigs from dams fed diets supplemented with algae or fish oil and challenged with LPS in late gestation

status: Public on Aug 14 2019

city: Guelph

first: Niel

last: Karrow

state: Ontario

address: 50 stone road east

department: Animal Biosciences

country: Canada

institute: University of Guelph

summary:
Maternal stress occuring during gestation can influence the functioning of the stress and immune responses in offspring. Maternal supplementation with immunomodulatory compounds such as omega-3 polyunsaturated fatty acids may reduce inflammation associated with maternal stress, promoting offspring health and growth
Sows were fed diets supplemented with microalgae or fish oil from gestation day 75 and were challenged with LPS on gestation day 112. Previously, LPS challenge in the male piglets of these sows resulted in differences in fever and cortisol responses among piglets from different maternal treatments. Therefore, the adrenal gland was chosen for microarray analysis to assess the effects of the maternal treatment on the gene expression within the hypothalamic-pituitary-adrenal axis.

overall_design: One male piglet per sow was selected to receive an LPS challenge one week after weaning (28 days of age). Two hours after LPS challenge, piglets were euthanized and adrenal tissue was collected for microarray analysis to assess the effects of maternal diet and LPS challenge on the adrenal transcriptome

first: Alison

middle: V

last: Lee

first: Lan

last: You

first: Layne

last: Harris

first: Kristen

last: Brennan


title: Discover of overlooked differentially expressed gene regions from single-cell RNA-seq data with neural stem cell derived from human induced pluripotent stem

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

institute: RIKEN

summary: Single-cell RNA sequencing has enabled researchers to quantify the transcriptomes of individual cells, infer cell types, and investigate differential expression among cell types, which will lead to a better understanding of the regulatory mechanisms of cell states. Transcript diversity caused by phenomena such as aberrant splicing events have been revealed, and the differential expression of previously unannotated transcripts might be overlooked by annotation-based analyses. Accordingly, we have developed an approach to discover overlooked differentially expressed (DE) gene regions that complements annotation-based methods. We applied our algorithm to two datasets and discovered several intriguing DE transcripts, including a transcript related to the modulation of neural stem/progenitor cell differentiation.

overall_design: Total 768 single cells (neural stem cell derived from human induced pluripotent stem) were sequenced by using RamDA-seq protocol.

first: Tetsutaro

last: Hayashi

first: Koki

last: Tsuyuzaki

first: Hirotaka

last: Matsumoto

first: Haruka

last: Ozaki

last: Nikaido


title: Transcritpional profiling of unstimulated and Candida albicans stimulated HoxER-PU.1 WT and HoxER-PU.1 KO neutrophils

status: Public on Mar 19 2019

city: Münster

first: Frank

last: Rosenbauer

address: Robert-Koch-Str. 43

department: Institute of Molecular Tumor Biology

institute: University Hospital Münster

summary: Neutrophils are essential first line defense cells against invading pathogens, yet their inappropriate activation contributes to immunological diseases and can cause collateral tissue damage. However, if and how neutrophils cell-intrinsically titrate their inflammatory response remains unknown. Here, we conditionally deleted PU.1, a key myeloid transcription factor, from the neutrophils of mice undergoing fungal infection, and then performed comprehensive epigenomic profiling. We find that a major function of PU.1 is to restrain the neutrophils’ immune response by broadly suppressing genomic enhancer outputs via recruiting histone deacetylase activity, thereby limiting the immune-stimulatory AP1-transcription factor JUNB from entering chromatin. Thus, neutrophils rely on a direct PU.1 repressor function as rheostat of the inflammatory chromatin state, safeguarding their epigenome from undergoing uncontrolled activation prior to pathogenic stimulation.

overall_design: mRNA profiles of unstimulated and C. albicans stimulated wildtype and PU.1 deleted neutrophils were generated by deep sequencing in duplicates or triplicates.

first: Josephine

last: Fischer

first: Carolin

last: Walter


title: Genome-wide binding profiles of JUNB in unstimulated HoxER-PU.1 WT and PU.1 KO neutrophils

summary: Neutrophils are essential first line defense cells against invading pathogens, yet their inappropriate activation contributes to immunological diseases and can cause collateral tissue damage. However, neutrophil-intrinsic mechanisms adjusting an appropriate inflammatory response are unknown. Herein, we conditionally deleted PU.1, a key myeloid transcription factor, from the neutrophils of mice undergoing fungal infection, and then performed comprehensive epigenomic profiling. We find that a major function of PU.1 is to restrain the neutrophils’ immune response by broadly suppressing genomic enhancer outputs via recruiting histone deacetylase activity, thereby limiting the immune-stimulatory AP1-transcription factor JUNB from entering chromatin. Thus, PU.1 acts as rheostat of the inflammatory chromatin state, safeguarding the neutrophil epigenome from undergoing uncontrolled activation prior to pathogenic stimulation.

overall_design: Examination of JUNB occupany in unstimulated HoxER-PU.1 WT and PU.1 KO neutrophils by deep sequencing in duplicates.


title: Genome-wide binding profiles of PU.1 in unstimulated and Candida albicans stimulated HoxER-PU.1 WT neutrophils

overall_design: Examination of PU.1 occupany in neutrophils prior and after stimulation by deep sequencing in duplicates.


title: Whole transcriptome profiling of neutrophils (Gr1+) flow-sorted from the BM of PU.1 WT and PU.1 KO mice

summary:
Neutrophils are essential first line defense cells against invading pathogens, yet their inappropriate activation contributes to immunological diseases and can cause collateral tissue damage. However, if and how neutrophils cell-intrinsically titrate their inflammatory response remains unknown. Here, we conditionally deleted PU.1, a key myeloid transcription factor, from the neutrophils of mice undergoing fungal infection, and then performed comprehensive epigenomic profiling. We find that a major function of PU.1 is to restrain the neutrophils’ immune response by broadly suppressing genomic enhancer outputs via recruiting histone deacetylase activity, thereby limiting the immune-stimulatory AP1-transcription factor JUNB from entering chromatin. Thus, neutrophils rely on a direct PU.1 repressor function as rheostat of the inflammatory chromatin state, safeguarding their epigenome from undergoing uncontrolled activation prior to pathogenic stimulation.
We performed whole transcriptome profiling of neutrophils (Gr1+) flow-sorted from the BM of PU.1 WT and PU.1 KO mice, and found nearly 1000 differentially expressed transcripts, 443 of which were decreased and 555 increased in PU.1-deleted neutrophils. Functional annotations of the differentially expressed transcripts revealed that differentiation-associated gene sets were not significantly changed in the neutrophils from PU.1∆Neu mice. In contrast, the top ranked gene ontology (GO) sets downregulated in PU.1∆Neu neutrophils represented immunological terms such as inflammatory response, NFκB activity and Toll-like receptor (TLR) signalling.

overall_design: Neutrophils were flow-sorted from PU.1 WT and PU.1 KO mice for RNA extraction and hybridization on Affymetrix microarrays.

first: Mathias

last: Leddin


title: RNA sequencing of mouse hepatic response to compounds with predicted lifespan-extending effect

status: Public on Jul 25 2019

city: Boston

first: Maxim

last: Gerashchenko

state: Massachusetts

address: 77 Louis Pasteur Ave, NRB 435

department: Medicine

institute: Brigham and Women's Hospital

summary: This dataset consists of hepatic gene expression profiles of mice subjected to 4 compounds predicted by Connectivity Map (CMap) using gene signatures identified for known lifespan-extending interventions: ascorbyl-palmitate, KU-0063794, AZD8055 and rilmenidine. Corresponding age-, sex- and strain-matched littermate controls are also presented.  Using this data, we confirmed the association between longevity signatures and gene expression response to the predicted compounds in vivo, using the same mouse model as for the identification of gene signatures associated with lifespan extension. This pilot project demonstrated the applicability of such approach for the discovery of new interventions with a desirable effect on gene expression and provided appealing candidates for further longevity studies.

overall_design: 3-month old UM-HET3 male mice from University of Michigan Medical School were subjected to ascorbyl-palmitate (6.3 ppm), KU-0063794 (10 ppm), AZD8055 (20 ppm) and rilmenidine (10 ppm) for 1 month. Their littermate controls of the same age and sex were also used for the analysis.  4 biological replicates were used for each treated group, while control samples included 8 biological replicates (24 samples in total). In all cases, interventions continued until the animals were sacrificed. RNA was extracted from liver tissues with PureLink RNA Mini Kit as described in the protocol and passed to CEL-seq.

first: Alexander

last: Tyshkovskiy

first: Perinur

last: Bozaykut

first: Vadim

middle: N

last: Gladyshev


title: Safeguard function of PU.1 shapes the inflammatory epigenome of neutrophils


title: Systematic identification of metabolites controlling gene expression in E. coli

status: Public on May 31 2019

city: Marburg

first: Hannes

last: Link

state: Hessen

address: Karl-von-Frisch Straße 16

department: Dynamic Control of Metabolic Networks

institute: MPI Marburg

summary: Cellular metabolism controls gene expression through allosteric interactions between metabolites and transcription factors. Methods to detect these regulatory interactions are mostly based on in vitro binding assays, but there are no methods to identify them at a genome-scale in vivo. Here we show that dynamic transcriptome and metabolome data identify metabolites that are potential effectors of transcription factors in E. coli. By switching the culture conditions between starvation and growth for 20 hours, we induced strong metabolite concentration changes and accompanying gene expression changes, which were measured by LC-MS/MS and RNA sequencing. From the transcriptome data we calculated the activity of 209 transcriptional regulators with Network Component Analysis, and then tested which metabolites correlated with these activities. This approach captured, for instance, the in vivo Hill-kinetics of CRP regulation by cyclic-AMP, a canonical example of allosteric transcription factor regulation in E. coli. By testing correlations between all pairs of transcription factors and metabolites, we predicted putative effectors of 65 transcription factors, and validated five of them in vitro. These results show that the combination of transcriptomics and metabolomics can generate hypotheses about metabolism-transcription interactions that are relevant in vivo and drive transitions between physiological states.

overall_design: Expression profiles of E. coli at 29 timepoints in duplicates during a perturbation experiment

first: Martin

last: Lempp


title: Identification of long noncoding RNA RP11-2B6.2 as a positive regulator of type I interferon pathway in lupus nephritis

status: Public on May 01 2019

city: Guangzhou

first: YY

last: Xiong

address: Xingangxi Rd

department: School of Life Sciences

institute: Sun Yat-sen University

summary: Methods and Materials  The high throughput RNA sequencing (RNA-seq) data from kidney biopsies of LN patients and controls was applied studied to screen for candidate lncRNAs. Quantitative real-time polymerase chain reaction(RT-qPCR) was used to detect the expression of lncRNAs and individual IFN-stimulated genes (ISGs). Western blotting and dual-luciferace luciferase reporter assay was  adopted to explore the specific function of the candidate lncRNA.     Results  The expression of lncRNA RP11-2B6.2 was significantly increased in the kidney tissues from LN patients compared with those from healthy controls, and positive correlated with the degree of disease activity and renal injuryinjuries. Additionally, expression of LncRNA RP11-2B6.2 could be stimulated by type I IFN. Silencing it RP11-2B6.2 significantly reduced the expression of a group of interferon-stimulating genes(ISGs) including IFIT1, OAS1, etc., Furthermore, it lncRNA RP11-2B6.2 affected the expression of IFN alpha and beta receptor subunit 1 (IFNAR1), phosphorylation of Jak1 and Stat1, and the luciferase activity induced by interferon stimulated response element(ISRE).    Conclusion  Long noncoding RNA RP11-2B6.2 is a positive regulator of the type I IFN signaling pathway in LN. It LncRNA RP11-2B6.2 may contribute to the pathogenesis of LN and provide served as a potentially therapeutic target.

overall_design: RNA-seq data from kidney biopsies of LN patients and controls was used to screen for candidate lncRNAs

first: Mengbiao

last: Guo

first: Zhuojun

last: Liao

first: Yuanjia

last: Tang


title: Transcriptome analysis reveals cotton (Gossypium hirsutum) genes that are differentially expressed in cadmium stress tolerance

status: Public on Apr 25 2019

city: Anyang

first: Mingge

last: Han

address: 38 Huanghe Avenue

institute: Institute of cotton research of CAAS,China

summary: For environmental safety, the high concentration of heavy metals in the soil should be removed. Cadmium (Cd), one of the heavy metals polluting the soil while its concentration exceeds 3.4 mg/kg in soil. Potential use of cotton for remediating heavy Cd-polluted soils is available while its molecular mechanisms of Cd tolerance remains unclear in cotton. In this study, transcriptome analysis was used to identify the Cd tolerance genes and their potential mechanism in cotton. Finally 4,627 differentially expressed genes (DEGs) in the root, 3,022 DEGs in the stem and 3,854 DEGs in leaves were identified through RNA-Seq analysis, respectively. These genes contained heavy metal transporter genes (ABC, CDF, HMA, etc.), annexin genes, heat shock genes (HSP) amongst others. Gene ontology (GO) analysis showed that the DEGs were mainly involved in the oxidation-reduction process and metal ion binding. The DEGs mainly enriched in two pathways, the influenza A and the pyruvate pathway. GhHMAD5 protein, containing a heavy-metal domain, was identified in the pathway to transport or to detoxify the heavy ion. GhHMAD5-overexpressed plants of Arabidopsis thaliana showed the longer roots compared with the control. Meanwhile, GhHMAD5-silenced cotton plants showed more sensitive to Cd stress compared with the control. The results indicated that GhHMAD5 gene is remarkably involved in Cd tolerance, which gives us a preliminary understanding of Cd tolerance mechanisms in upland cotton. Overall, this study provides valuable information for the use of cotton to remediate the soil polluted with heavy metals.

overall_design: leaf, stem and whole root of  three leaf-heart cotton seedlings were collected for 9h under 4 mM CdCl2 solution.

first: Wuwei

last: Ye


title: RNA-Sequencing Quantitative Analysis of Mice Wild Type and Tg-ACE (ACE overexpression) Macrophages

status: Public on Jan 18 2019

city: West Hollywood

first: AGCT

last: Core

address: 8687 Melrose Ave, PDC B230

institute: Cedars Sinai Medical Center

summary: In this study we compared transcriptome profiling (RNA-seq) in wild type vs. ACE overexpressiong Tg-ACE macrophages to identify differential gene expression/pathways.

overall_design: RNA-Seq analysis of WT vs. Tg-NKO macrophages (n=3 each group)

first: Zakir

last: Khan

first: Kenneth

last: Bernstein


title: Single-Cell Transcriptome Analysis Maps the Developmental Track of the Human Heart

status: Public on Jan 25 2019

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

summary:
The heart is the central organ of the circulatory system, and its proper development is vital for maintaining human life. Here we used single-cell RNA-sequencing to profile the gene expression landscapes of ~4,000 cardiac cells from human embryos and identified four major types of cells: cardiomyocytes (CMs), cardiac fibroblasts, endothelial cells (EC) and valvar interstitial cells (VICs). During heart development, atrial and ventricular CMs acquired distinct features early in development. Furthermore, both CMs and fibroblasts show stepwise changes in gene expression. As development proceeds, VICs might be involved in the remodeling phase, and ECs display location-specific characteristics. Finally, we compared gene expression profiles between human and mouse and identified a serial of unique features of human heart development. Our study lays the groundwork for elucidating the mechanisms of in vivo human cardiac development and provides potential clues to understand cardiac regeneration.
The gene expression pattern of our data can be easily viewed and navigated at https://tanglab.shinyapps.io/human_fetal_heart_scRNA/.

overall_design:
single cell RNA seq data set 1: 77 samples
single cell RNA seq data set 2: 21 samples

first: Yueli

last: Cui

first: Xixi

last: Liu

first: Liying

last: Yan

first: Xiaoying

last: Fan

first: Jun

last: Yong

first: Yuqiong

last: Hu

first: Ji

last: Dong

first: Qingqing

last: Li

first: Xinglong

last: Wu

first: Shuai

last: Gao

first: Jingyun

first: Lu

last: Wen

first: Jie

last: Qiao

first: Fuchou


title: Genome-wide maps of chromatin state in unstimulated HoxER-PU.1 WT and HoxER-PU.1 KO neutrophils

first: Frank

last: Rosenbauer

overall_design: Examination of 2 different histone modifications in unstimulated HoxER-PU.1 WT and HoxER-PU.1 KO neutrophils by deep sequencing in duplicates.

first: Josephine

last: Fischer

first: Carolin

last: Walter


title: The transcription factor BATF3 regulates the differentiation of TH9 cells and TH9-driven mucosal pathologies

status: Public on Jan 08 2019

first: AGCT

last: Core

summary: T helper 9 (TH9) cells are important for the development of inflammatory and allergic diseases. The TH9 transcriptional network converge signals from cytokines and antigen presentation but is incompletely understood. Here, we identified TL1A, a member of the TNF superfamily, as strong inducer of mouse and human TH9 differentiation. Mechanistically, TL1A induced the expression of the transcription factors BATF and BATF3 and facilitated their binding to the Il9 promoter leading to enhanced secretion of IL-9. BATF- and BATF3-deficiencies impaired IL-9 secretion under TH9 and TH9-TL1A polarizing conditions. In vivo, using a T cell transfer model we demonstrated that TL1A promoted IL-9-dependent, TH9 cell-induced intestinal and lung inflammation. Neutralizing IL-9 antibodies attenuated TL1A-driven mucosal inflammation. Batf3-/- TH9-TL1A cells induced reduced inflammation and cytokine expression in vivo compared to WT cells. Our results demonstrate that TL1A promotes TH9 cell differentiation and function and define a role of BATF3 in TH9-induced mucosal inflammation.

overall_design: 4 samples (2x2)

first: Masato

last: Tsuda

first: Kathrin

last: Michelsen

last: Tang

first: Yizhou

last: Wang


title: Bronchial premalignant lesions have distinct molecular subtypes associated with future histologic progression

status: Public on Mar 05 2019

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

summary: Exposure to cigarette smoke creates a field of injury throughout the entire respiratory tract inducing genomic alterations that lead to an “at-risk” airway where and lung cancers develop.  Lung squamous cell carcinoma (SCC) arises in the epithelial layer of the bronchial airways and is often preceded by the development of premalignant lesions(PMLs). The presence of high-grade persistent or progressive PMLs is a marker of increased lung cancer risk both at the lesion site elsewhere in the lung.  Effective tools to identify and treat premalignant lesions at highest risk of progression to invasive carcinoma are lacking.  We profiled via RNA-Seq airway brushing and biopsies (divided into two cohorts: discovery and validation) obtained from high-risk smokers undergoing lung cancer screening via serial auto-fluorescence bronchoscopy procedures. We identified four distinct molecular subtypes (Proliferative, Inflammatory, Secretory, and Normal) in the bronchial biopsies that correspond to a spectrum of biological and morphological alterations.   The Proliferative subtype was enriched with dysplastic PMLs from current smokers that exhibit up-regulation of KRT5 and KI67 as well as metabolic and cell cycle pathways, and down-regulation of cilium-associated processes and FOXJ1 expression.  Molecular subtype classification in the validation cohort biopsies replicated these significant clinical and biological associations.  Airway brushes from normal fluorescing areas of the large airway classified as the Proliferative subtype specifically predicts the presence of biopsies of this same subtype.  Within the Proliferative subtype, genes associated with interferon signaling and antigen processing and presentation were observed to be down-regulated among dysplastic biopsies that persistent or progress in the future.  Innate and adaptive immune cells were computationally predicted to be depleted in these biopsies and this was confirmed via immunofluorescence staining of adjacent biopsies.  These findings provide a proof of concept that molecular biomarkers of endobronchial biopsies can enhance histopathological grading and that immunoprevention strategies are an important future direction in intercepting the progression of PMLs to lung cancer.

overall_design:
Endobronchial biopsies and brushings were obtained from high-risk subjects undergoing lung cancer screening at approximately 1-year intervals by white light and auto-fluorescence bronchoscopy and computed tomography at the Roswell Park Cancer Institute in Buffalo, NY.  Subjects were selected that had biopsies collected in repeat locations via serial bronchoscopies. mRNA sequencing was performed on a discovery cohort (DC) of samples comprising of endobronchial biopsies and brushes collected between 2010 and 2012 (n=30 subjects, n=197 biopsies, and n=91 brushings).  mRNA sequencing was subsequently performed on a validation cohort (VC) of samples comprising of endobronchial biopsies and brushes collected between 2010 and 2015 (n=20 subjects, n=111 biopsies, and n=49 brushings).

The submitter declares that the raw data will be made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap) due to patient privacy concerns.

first: Jennifer

last: Beane

first: Avrum

last: Spira


title: Change of gene expression of mutation of TP53 in LS174T cells

status: Public on Dec 26 2018

city: yushima bunnkyoku Tokyo

first: Sho

last: Watanabe

department: gastroenterology

institute: Tokyo medical and dental university

summary: Change of gene expression of mutation on TP53 exon3 or exon10 by CRISPR-Cas9 system in LS174T cells

overall_design: TP53Exon3 and TP53 Exon10 mutated LS174T cells were compared with TP53WT LS174T cells.

first: Kiichiro

last: Tsuchiya


title: The 3' end processing factor PCF11 regulates gene expression based on gene size and intronic polyadenylation

status: Public on Feb 12 2019

city: Newark

first: Bin

last: Tian

state: NJ

address: 205 South Orange Ave.

department: Department of Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers New Jersey Medical School

summary: Genes with different sizes have distinct expression patterns and functions. Here we show that the 3' end processing PCF11 modulates gene expression according to gene size. Gene density and polyA site strength, but not orientation between neighboring genes, impact short gene regulation by PCF11. In contrast, long gene modulation involves intronic polyadenylation (IPA), which is widespread in large introns. Downregulation of PCF11, which takes place in cell differentiation, contributes to short and long gene expressions with functions related to cell proliferation, cell morphology, adhesion, and migration. Mild, exogenous upregulation of PCF11 perturbs the gene expression program in cell differentiation. Further, PCF11 is auto-regulated through a highly conserved IPA site, the removal of which leads to PCF11 overexpression and global activation of proximal PASs sites. Together, our data indicate that PCF11 level impacts gene expression based on size and its autoregulation maintains homeostasis of PAS usage in the cell.

overall_design:
In total 2 RNA-seq libraries from 3T3-L1 cells for gene expression analysis;
In total 4 3'READS libraries for the analysis of APA during C2C12 cell differentiation;
In total 4 3'READS libraries for analysis of APA isoform stability under siPcf11 using 4sU metabolic labeling in C2C12 cells;
In total 4 3'READS libraries for analysis of APA under siPcf11 using total RNA from C2C12 cells;
In total 4 3'READS libraries for analysis of APA under Pcf11-IPAKO using total RNA from 4T1 cells;
In total 4 3'READS libraries for analysis of APA under siPcf11 using total RNA from NIH3T3 cells;

first: Ruijia

first: Dinghai

last: Zheng

first: Lv

last: Wei

first: Qingbao

last: Ding


title: Malaria Host Pathogen Center Experiment 07A and 07B - Macaca fascicularis infected with Plasmodium knowlesi to produce and integrate clinical, hematological, parasitological, omics, telemetric and histopathological measures of acute primary infection.

status: Public on Mar 14 2019

city: Atlanta

first: Mary

last: Galinski

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

institute: Emory University

summary: This project is part of the Malaria Host-Pathogen Interaction Center (MaHPIC) - a transdisciplinary malaria systems biology research program initially supported by an NIH/NIAID contract (# HHSN272201200031C, 2012-2017; see http://www.systemsbiology.emory.edu). The MaHPIC has continued with support from the Defense Advanced Research Project Agency (DARPA) and others. The MaHPIC generates many data types (e.g., clinical, hematological, parasitological, metabolomics, functional genomics, lipidomics, proteomics, immune response, telemetry) and mathematical models, to iteratively test and develop hypotheses related to the complex host-parasite dynamics in the course of malaria in non-human primates (NHPs), and metabolomics data via collaborations with investigators conducting clinical studies in malaria endemic countries, with the overarching goal of better understanding human disease, pathogenesis, and immunity. Curation and maintenance of all data and metadata are the responsibility of the MaHPIC.

sample_organism:
Plasmodium knowlesi
Macaca fascicularis
Macaca mulatta

overall_design: The E07 cohort was inoculated with freshly dissected P. knowlesi sporozoites on 11/01/16. However, for unexplained reasons blood-stage parasitemias did not occur. Consequently, the E07 cohort was reinoculated with cryopreserved P. knowlesi sporozoites. This inoculation was performed on 1/20/17.  Hence 'E07A' refers to samples and results from the failed inoculation from 11/01/16 and 'E07B' refers to samples and results from the successful inoculation on 1/20/17).  Telemetry devices (DSI, model L11) with blood pressure sensors and electrocardiogram (ECG) leads were surgically implanted in seven malaria-naive male long-tailed macaques (Macaca fascicularis), approximately five years of age.  After a resting period of three weeks, the telemetry implants were turned on and physiological data that include activity, temperature, ECG, and blood pressure were continuously collected.  After the E07A failed infection using a fresh preparation of salivary gland sporozoites, the implants were deactivated to preserve battery life. Between E07A and E07B, a single rhesus macaque (M. mulatta) was added to the cohort as an infection control with no telemetry implant.  At the start of E07B, telemetry implants were reactivated.  Ten days after reactivation all animals were inoculated intravenously with cryopreserved P. knowlesi Malayan strain salivary gland sporozoites, obtained from Anopheles dirus infected with parasites from the Pk1A+ clone and previously tested in E30 for their infectivity of macaques. The sporozoite stocks used were produced, isolated and cryopreserved at the Centers for Disease Control and Prevention, and then stored at Yerkes.  After inoculation, the macaques were profiled for clinical, hematological, parasitological, immunological, functional genomic, proteomic, and metabolomic measurements.  The experiment was designed with pathology studies and thus terminal necropsies, which were scheduled at the log phase of the infection, at the peak of parasitemias, at the middle of the chronic phase, or at the end of the follow-up period of 45 days after the inoculation of the sporozoites.  Capillary blood samples were collected daily for the measurement of complete blood counts (CBCs), reticulocytes, and parasitemias.  Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis.  Venous blood and bone marrow samples were collected at six time points for functional genomic, targeted proteomic, targeted metabolomics, and immunological analyses.  Physiological data noted above were continuously captured via telemetry. Within the MaHPIC, this project is known as ‘Experiment 07 (E07A and 07B)’.  This dataset was produced by Dr. Steven E. Bosinger, Nirav Patel, and Gregory K Tharp at the Emory University Yerkes Genomics Core. To access other publicly available results from ‘E07' and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp .  This page will be updated as datasets are released to the public.  The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC) and the MRMC Office of Research Protection Animal Care and Use Review Office (ACURO).  This dataset contains results from both E07A and E07B.

first: John

last: Barnwell

first: Steven

middle: E

last: Bosinger

first: Monica

last: Cabrera-Mora

first: Regina

last: Cordy

first: Jeremy

last: DeBarry

first: Allison

last: Hankus

first: Jay

last: Humphrey

first: Nicolas

last: Lackman

first: Stacey

last: Lapp

first: Alberto

last: Moreno

first: Mustafa

last: Nural

first: Suman

last: Pakala

first: Nirav

last: Patel

first: Chester

last: Joyner

first: Mariko

last: Peterson

first: Gregory

last: Tharp

first: Jianlin

last: Jiang

first: Juan

last: Gutierrez

first: Rabindra

last: Tirouvanziam


title: Malaria Host Pathogen Center Experiment 06: Macaca mulatta infected with Plasmodium knowlesi sporozoites to produce and integrate clinical, hematological, parasitological, omics, telemetric, and histopathological measures of acute primary infection.

status: Public on Mar 01 2019

first: Mary

last: Galinski

sample_organism:
Plasmodium knowlesi
Macaca mulatta

platform_organism:
Plasmodium knowlesi
Macaca mulatta

overall_design: Telemetry devices (DSI, model L11) with blood pressure sensors and electrocardiogram (ECG) leads were surgically implanted in four malaria-naive male rhesus macaques (Macaca mulatta), approximately five years of age.  After a resting period of two weeks, physiological data that include activity, temperature, ECG, and blood pressure were continuously collected. Two weeks after activation of the telemetry implant, the macaques were inoculated intravenously with cryopreserved P. knowlesi Malayan strain salivary gland sporozoites, obtained from Anopheles dirus infected with parasites from the Pk1A+ clone and previously tested in E30 for their infectivity of macaques. The sporozoite stocks used were produced, isolated and cryopreserved at the Centers for Disease Control and Prevention, and then stored at Yerkes. After inoculation, the macaques were profiled longitudinally for clinical, hematological, parasitological, immunological, functional genomic, proteomic, and metabolomic measurements. The experiment was designed with pathology studies and thus terminal necropsies, which were scheduled at the log phase of the infections or at the peak of parasitemias. Capillary blood samples were collected daily for the measurement of complete blood counts, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomics analyses. Venous blood and bone marrow samples were collected at five timepoints for functional genomic, targeted proteomic, targeted metabolomics, and immunological analyses. Physiological data noted above were continuously captured via the implanted telemetry devices.  Within the MaHPIC, this project is known as ‘Experiment 06’. This dataset was produced by Dr. Steven E. Bosinger, Nirav Patel, and Greg Tharp at the Emory University Yerkes Genomics Core. To access other publicly available results from E06 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp.  This page will be updated as datasets are released to the public.  The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC) and the MRMC Office of Research Protection Animal Care and Use Review Office (ACURO).

first: John

last: Barnwell

first: Steven

last: Bosinger

first: Monica

last: Cabrera-Mora


title: Amyloid-β42-induced neurodegeneration enhances stem cell plasticity and neurogenesis in adult zebrafish brain

status: Public on Dec 22 2018

first: Caghan

last: Kizil

state: NY

institute: Columbia University Irving Medical Center

summary: To analyze the effects of Ab42-mediated neurodegeneration in adult zebrafish brain, we generated an Ab42 deposition model and analyzed the transcriptome of stem cells and parenchymal cells.

overall_design: 6 months old Tg(her4.1:EGFP) adult fish brains were injected with CPP or AB42 using CVMI method (Kizil etal, 2013). 48 hpi brains were dissected, dissocited and non-GFP (GFP-N) and GFP positive (GFP-P) cells were sorted with FACS. Following total RNA isolation, samples were sequenced with triple replicates on Illumina HiSeq 2000 platform (75 bp end-read).

first: Prabesh

last: Bhattarai

first: Mehmet

last: Cosacak

first: Andreas

last: Dahl


title: RNA-seq transcriptional profiling in primary human hepatocyte(in vitro/in vivo) and Proliferting human hepatocyte(in vitro/in vivo)

status: Public on Dec 19 2018

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

summary: The source of human hepatocytes (HHs) is limited because of the shortage of donor organs and the difficulty to expand them in vitro. We developed a defined medium to expand HHs for about 10,000-fold in numbers. The proliferating HHs are bi-phenotypic, showing partially maintained hepatic features and additionally gained expression of progenitor-associated genes. Importantly, proliferating HHs extensively engraft in injured mouse livers at the level comparable to primary HHs. Moreover, these cells are matured upon transplantation in vivo or differentiation in maturation medium in vitro.

overall_design: During the culture process,  transcriptional profiling in PHH and different passages proliHHs were generated by RNA-seq analysis. Transcriptional profiling in PHH and ProliHH-repopulated Fah-/-Rag2-/-IL2rg-/- mouse liver were generated by RNA-seq analysis.

first: Kun

last: Zhang

first: Ludi